Species-specific tuning increases robustness to sampling bias in models of species distributions: An implementation with Maxent

Various methods exist to model a species’ niche and geographic distribution using environmental data for the study region and occurrence localities documenting the species’ presence (typically from museums and herbaria). In presence-only modelling, geographic sampling bias and small sample sizes represent challenges for many species. Overfitting to the bias and/or noise characteristic of such datasets can seriously compromise model generality and transferability, which are critical to many current applications - including studies of invasive species, the effects of climatic change, and niche evolution. Even when transferability is not necessary, applications to many areas, including conservation biology, macroecology, and zoonotic diseases, require models that are not overfit. We evaluated these issues using a maximum entropy approach (Maxent) for the shrew Cryptotis meridensis, which is endemic to the Cordillera de Mérida in Venezuela. To simulate strong sampling bias, we divided localities into two datasets: those from a portion of the species’ range that has seen high sampling effort (for model calibration) and those from other areas of the species’ range, where less sampling has occurred (for model evaluation). Before modelling, we assessed the climatic values of localities in the two datasets to determine whether any environmental bias accompanies the geographic bias. Then, to identify optimal levels of model complexity (and minimize overfitting), we made models and tuned model settings, comparing performance with that achieved using default settings. We randomly selected localities for model calibration (sets of 5, 10, 15, and 20 localities) and varied the level of model complexity considered (linear versus both linear and quadratic features) and two aspects of the strength of protection against overfitting (regularization). Environmental bias indeed corresponded to the geographic bias between datasets, with differences in median and observed range (minima and/or maxima) for some variables. Model performance varied greatly according to the level of regularization. Intermediate regularization consistently led to the best models, with decreased performance at low and generally at high regularization. Optimal levels of regularization differed between sample-size-dependent and sample-size-independent approaches, but both reached similar levels of maximal performance. In several cases, the optimal regularization value was different from (usually higher than) the default one. Models calibrated with both linear and quadratic features outperformed those made with just linear features. Results were remarkably consistent across the examined sample sizes. Models made with few and biased localities achieved high predictive ability when appropriate regularization was employed and optimal model complexity was identified. Species-specific tuning of model settings can have great benefits over the use of default settings.     

Immunoassay-based screening of polychlorinated biphenyls (PCB) in sediments: requirements for a new generation of test kits

Polychlorinated biphenyls (PCBs) have been proposed for the inclusion in the European Water Framework Directive (WFD) priority list, currently under revision. Various screening methods have been employed for PCB determination in different environmental matrixes in the last decades, immunoassays being one of the most employed. A literature review reveals that the enzyme-linked immunosorbent assay (ELISA) is the most commonly applied immunoassay for PCB determination in the environment. However, its application to sediments is very limited. A suitability assessment of immunoassay-based analysis for PCB screening in sediments is presented in this work. The significance of available immunoassay-based test kits under the current environmental pollution scenario and their performance against the sensitivity and specificity requirements dictated by the WFD for PCB analysis in sediments is discussed. For example, current detection limits of available test kits for PCB determination in sediments may not be enough for compliance checking under the WFD. In addition, concentration expressed as Aroclor equivalents does not seem to be the way forward. A proposal for adapting available test kits in order to become more suitable tools for PCB screening in sediments is also presented in this study.     

Using selection functions to describe changes in environmental variables

The selection function (which shows how the frequency of sampling units with the value X = x at one point in time must change in order to produce the distribution that occurs at a later point in time) is proposed for describing the changes over time in an environmentally important variable X. It is shown that the theory of selection functions as used in the study of natural selection and resource selection by animals requires some modifications in this new application and that a selection function is a useful tool in long-term monitoring studies because all changes in a distribution can be examined (rather than just changes in single parameters such as the mean), and because graphical presentations of the selection function are easy for non-statisticians to understand. Estimation of the selection function is discussed using a method appropriate for normal distributions and bootstrapping is suggested as a method for assessing the precision of estimates and for testing for significant differences between samples taken at different times. Methods are illustrated using data on water chemical variables from a study of the effects of acid precipitation in Norway.     

Factors Related to Spatial Patterns of Rural Land Fragmentation in Texas

Fragmentation of family-owned farms and ranches has been identified as the greatest single threat to wildlife habitat, water supply, and the long-term viability of agriculture in Texas. However, an integrative framework for insights into the pathways of land use change has been lacking. The specific objectives of the study are to test the hypotheses that the nonagricultural value (NAV) of rural land is a reliable indicator of trends in land fragmentation and that NAV in Texas is spatially correlated with population density, and to explore the idea that recent changes in property size patterns are better represented by a categorical model than by one that reflects incremental changes. We propose that the State-and-Transition model, developed to describe the dynamics of semi-arid ecosystems, provides an appropriate conceptual framework for characterizing categorical shifts in rural property patterns. Results suggest that changes in population density are spatially correlated with NAV and farm size, and that rural property size is spatially correlated with changes in NAV. With increasing NAV, the proportion of large properties tends to decrease while the area represented by small properties tends to increase. Although a correlation exists between NAV and population density, it is the trend in NAV that appears to be a stronger predictor of land fragmentation. The empirical relationships established herein, viewed within the conceptual framework of the State-and-Transition model, can provide a useful tool for evaluating land use policies for maintaining critical ecosystem services delivered from privately owned land in private land states, such as Texas.     

Microbial communities and immigration in volcanic environments of Canary Islands (Spain)

Volcanic eruptions originated the Canary Islands (Spain), and today, different landscapes clearly show that active volcanism. The microbial communities present in these volcanic environments, both at high (above 70 degrees C) and moderate (25-35 degrees C) temperatures, were analyzed. Rock samples were processed using molecular techniques based on both DNA and RNA and complemented with the culture of microorganisms at a wide range of temperatures. Microorganisms detected through RNA-based molecular surveys were mostly related to mesophilic microorganisms, while representatives of hyperthermophiles were not detected. RNA decay curves at 80 degrees C resulted in half-life estimates of less than 2 min for mesophilic microorganisms, supporting a recent and continuous arrival of microorganisms to the high temperature sampled sites. This study constitutes a unique experimental approach showing a great natural potential of microorganisms to spread out to different natural environments. The implications are of great interest for the biogeography, dispersal, and potential distribution of microorganisms, and their genetic information, in natural environments.     

Responses of an estuarine population of the blue mussel Mytilus edulis to heated water from a steam generating plant

An entire bed of the blue mussel Mytilus edulis, consisting of 5,000 individuals/m², died during June, 1971 in the effluent canal of a steam generating plant when the temperature increased above 27°C. Similarly, the population in the intake canal disappeared when temperatures rose above 27°C in August. Laboratory studies showed that M. edulis could not tolerate continuous temperatures above 27°C, and feeding stopped shortly after the mussels were exposed to 25°C. Histopathological studies indicated that the cause of death of this bivalve was associated with degeneration of the frontal and laterofrontal cilia of the columnar epithelium of the gill filaments. In conjuction with this, there was necrosis and sloughing of the epithelium of the intestinal diverticula. Extensive amoebocytic infiltration was noted in the byssogenous cavity, gill filaments and stomach wall.This paper represents part of a dissertation by the first author, submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, University of Rhode Island, January 1973.     

Aquatic habitat modifications in La Plata River basin, Patagonia and associated marine areas

This paper describes the environmental characteristics and situation of aquatic habitats and communities in southern continental and maritime areas of southeastern South America (Patagonian Shelf GIWA Subregion), resulting from an overall assessment carried out within the framework of a GIWA project, mostly on the basis of publicly available data. The main focus of the analysis was on the current situation of transboundary water resources and anthropogenic impacts. In the inland waters, habitat and community modifications result, principally, from dams and reservoirs built in the main watercourses for hydroelectric power generation and other uses. The transformation of lotic environments into lentic ones have affected habitats and altered biotic communities. In the La Plata River basin, invasive exotic species have displaced native ones. Habitats in the ocean have been degraded, as their biodiversity becomes affected by overfishing and pollution. This article includes a discussion on the causal chain and the policy options elaborated for the Coastal Ecosystem of Buenos Aires province and the Argentinean-Uruguayan Common Fishing Zone, where fishing resources are shared by both countries.     

Gluconic acid production and phosphate solubilization by the plant growth-promoting bacterium<Emphasis Type="Italic"> Azospirillum</Emphasis> spp.

In vitro gluconic acid formation and phosphate solubilization from sparingly soluble phosphorus sources by two strains of the plant growth-promoting bacteria A. brasilense (Cd and 8-I) and one strain of A. lipoferum JA4 were studied. Strains of A. brasilense were capable of producing gluconic acid when grown in sparingly soluble calcium phosphate medium when their usual fructose carbon source is amended with glucose. At the same time, there is a reduction in pH of the medium and release of soluble phosphate. To a greater extent, gluconic acid production and pH reduction were observed for A. lipoferum JA4. For the three strains, clearing halos were detected on solid medium plates with calcium phosphate. This is the first report of in vitro gluconic acid production and direct phosphate solubilization by A. brasilense and the first report of P solubilization by A. lipoferum. This adds to the very broad spectrum of plant growth-promoting abilities of this genus.     

Bacterial communities of the marine sponges Hymeniacidon heliophila and Polymastia janeirensis and their environment in Rio de Janeiro, Brazil

In this study we performed a survey of the bacterial communities associated with the Western Atlantic demosponges Hymeniacidon heliophila and Polymastia janeirensis, based on 16S rRNA sequencing and transmission electron microscopy (TEM). We compared diversity and composition of the sponge-associated bacteria to those of environmental bacteria, represented by free-living bacterioplankton and by bacteria attached to organic particulate matter in superficial sediments. Partial bacterial 16S rRNA sequences from seawater, sediment, and sponges were retrieved by PCR, cloning, and sequencing. Sequences were subjected to rarefaction analyses, phylogenetic tree construction, and LIBSHUFF quantitative statistics to verify coverage and similarity between libraries. Community structure of the free-living bacterioplankton was phylogenetically different from that of the sponge-associated bacterial assemblages. On the other hand, some sediment-attached bacteria were also found in the sponge bacterial community, indicating that sponges may incorporate bacteria together with sediment particles. Rare and few prokaryotic morphotypes were found in TEM analyses of sponge mesohyl matrix of both species. Molecular data indicate that bacterial richness and diversity decreases from bacterioplankton, to particulate organic sediment, and to H. heliophila and P. janeirensis. Sponges from Rio de Janeiro harbor a pool of novel and exclusive sponge-associated bacterial taxa. Sponge-associated bacterial communities are composed of both taxons shared by many sponge groups and by species-specific bacteria.